After returning to Bloquear from her adventures in the previous book, Nya Analove enrolls at Bloquear University. She is thrilled to find that Zach Dare is also going to the Uni. Harry James is their tour guide, showing them around. Zach takes an interest in swordsmanship, while Nya chooses potions and archery. As she gets used to Uni life, Nya meets many friends, like the pretty Jordan Glass, the shy Gemma Redd, the nice Vent Arthur, and the mean Ethan. However, Mackenzie Reed, a student, is attacked, and she mumbled about "white eyes." Soon Nya's wielder powers are acting up again, and she flies during archery class. Zach, who is an Expert in Swordsmanship, fears Herobrine isn't dead. Nya starts to have Herobrine dreams again.
During a potions class, Nya becomes sick after the teacher, Mr. Ranger, shows the class a red potion (actually the one that made Nya a wielder). She finds comfort in her dorm friends Clare Jones and Emerald. During a hang-out with Emerald and Zach, Nya runs into her sister Tali, who she hasn't seen in a long time. When she goes home, a Herobrine nightmare leads her to burn down her apartment with her Wielder powers. She has to move into the Analove house, and have dinner with her cold father and caring mother. Tali, in a surprise, tells Nya she is dating Harry. Harry and Tali start to date. Mr. Ranger then attacks Nya after class with Herobrine's sword, and his eyes become white. He says he is serving his mistress, and Emerald told him her to come to see him. Emerald the next day stabs Zach, and no one knows why. Another time, Ranger tells Nya that the mistress is close to her. Emerald is able to warn Nya and takes her to the library. While there, she finds a terrified Mackenzie trying to warn her. In a cliffhanger, the evil mistress is revealed to be Clare.
Clare says that she heard Herobrine's voice in the library at the year's beginning, and was convinced to become a wielder. She introduces Nya to Special Energies (SE); the special power that wielders have. Claire has the power of Mind Manipulation, which allowed her to control Mr. Ranger and Emerald to do her bidding. Nya has Fire Manipulation, such to the point that Clare is impressed. After escaping and trying to explain this all to Zach, Tali reveals she and Harry are now engaged. Nya then tells her full story from Book 1 and says that Herobrine is not a myth. She shows her sister a piece of paper Clare dropped in the hall, with an address. Nya and Mackenzie find the street and building, Ol John's Potions Brewery. Connor the clerk says that Clare was there, and she was raging and screaming over dissapointing someone and a dead body. After meeting up with Zach, they part ways for school. At night, Tali and Harry plan to break into Bloquear University to steal Clare's file record. They succeed (barely being caught). The next day, Nya overhears Clare talking to Herobrine's voice, plotting to kill Tali to weaken Nya. Tali meets with Nya, but while explaining Clare's file, starts stabbing herself. A horrified Nya and Harry try to stop her (being controlled by Clare), but to no avail. Nya and Harry cry and mourn over Tali's death, and plan to stop Herobrine/Clare for good. Meanwhile, Herobrine (upset that other people saw Tali die) and Clare plan to deal with Zach.
A new kid, Alex, joins Nya's archery class. Nothing is helping, though, as Nya and her friends are trying to get over Tali's death. The next day, with help from Alex, Nya gets a note from a teacher to get into the restricted library section, where Clare has been borrowing the same book from. The book turns out to hold Clare's diary, which explains she met Herobrine as "Steve" (like Nya), but then found out he was evil and was imprisoned in his Nether palace. Alex then appears and reveals himself to be Herobrine. He opens a portal to the Nether, taking Nya with him and imprisoning him. He then tells Nya why he is bent on revenge and hates her so much.
Herobrine knew Nya's destiny to be a wielder beforehand, and wanted to bring that power out. After hundreds of failed one-time wielders, Herobrine came up with the Sangue Rosso to make an immortal wielder. Having fallen in love with Nya, he wanted to test it on her, but she betrayed him. His potion brewer's will said to finish the Sangue Rosso, as the one Herobrine gave Nya in the jungle was a prototype. The new one was used on Clare. With the Sangue Rosso, he plans to create an army of wielders and create a monarchy of Minecraftia. Back in the Uni, Clare knocks out Zach with a shovel and takes him to the Nether palace. From behind an invisible wall, Herobrine and Clare await the "final part of the revenge." Herobrine clouds Nya's mind, and then moves her to a room trapped with Jordan, Vent, Gemma, Ethan, and Emerald. Clare comes in and uses her Mind Manipulation SE to turn Nya's friends into her servants. From behind the invisible wall, Nya watches Zach duel the students in an epic sword fight (what Herobrine wants). He uses this distraction to try to possess Zach. Nya, slowly growing in her Fire SE, tries to burn through the invisible wall. During Zach's struggle, Herobrine fails to possess him, owing to the fact that Herobrine himself is in a weakened state. Clare, who is straining from the mind control SE, tries to convince Herobrine to stop, as he is becoming arrogant. However, he plots to gain Nya's body and wage war on Minecraftia. Clare loses some control over the students during this argument. When Herobrine tries to possess Nya, he fails and realizes that she has 2 SEs: Fire Manipulation and a mental block (extremely rare).
Near defeat, Herobrine turns to Clare, asking to posses her body. Clare refuses, saying it was not part of the deal to be his body. Nya then realizes Clare is lost, not evil, and she does not have to be Herobrine's wielder. During the fight, Clare starts to rebel, going to the point of making Jordan shoot Herobrine. He touches on the sensitive subject of Clare's parents' deaths at the hands of mobs. Nya then realizes that Herobrine, having control over the mobs after wandering alone as a teen, was the one who killed Clare's parents. A horrified Clare has a flashback of her parents' deaths and the depression afterwards; it was all so that Herobrine could befriend her and make her a wielder. She turns on Herobrine and leads everyone in a fight against him, even though it could kill her. They manage to shoot (Mackenize), stab (Ethan), and burn (Nya) Herobrine, but he survives. Mackenzie sacrifices herself to protect Nya, whose SE has grown to the point she is using her fire to burn down the Nether palace. Clare and Nya realize that Herobrine is immortal and can only be halted not stopped. In a heartbreaking moment, Clare decides to stay behind, planning to use her Mind Manipulation SE to destroy the palace. Nya and Clare part ways, as the students head to a Nether portal to escape. In the final moments of the book, Clare realizes she has done evil as a wielder and regrets it. The dying Herobrine watches his palace get destroyed. Herobrine then has visions of his friend Alex, who died being evil, and he sees how his fate is the same. The book ends with Clare hoping she will be remembered not as a villain, but as the girl who died for good.
Herobrine's Legacy is the third and final book of the series, and a sequel to Herobrine's Revenge. The story continues the tale of Nya and Zach Dare along with their children Kai and Tail Dare.